Variant report

Variant	rs7754459
Chromosome Location	chr6:23583630-23583631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1000105	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014989	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193599	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12200767	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12201667	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12212208	0.84[EUR][1000 genomes]
rs12213279	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215692	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17499234	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17499906	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17499955	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923197	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923198	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197966	0.84[ASN][1000 genomes]
rs197968	0.84[ASN][1000 genomes]
rs199079	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs199081	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs199124	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57279011	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58834120	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59488676	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456557	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917610	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746629	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7746858	0.93[EUR][1000 genomes]
rs7766899	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877615	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9460898	0.83[EUR][1000 genomes]
rs9466849	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9466850	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9466852	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422291	chr6:23466080-23600459	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv830608	chr6:23558655-23644405	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7754459	HIST1H4I	cis	cerebellum	SCAN
rs7754459	PPAPDC3	trans	lymphoblastoid	seeQTL
rs7754459	ACOT13	cis	parietal	SCAN
rs7754459	HIST1H2BB	cis	cerebellum	SCAN
rs7754459	HIST1H2AA	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:23579600-23584000	Weak transcription	Fetal Intestine Large	intestine
2	chr6:23579600-23584400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:23582400-23585000	Active TSS	Liver	Liver
4	chr6:23583000-23584000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:23583200-23585800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:23583600-23583800	Enhancers	Fetal Intestine Small	intestine

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